Mercurial > repos > iuc > data_manager_salmon_index_builder

annotate data_manager/salmon_index_builder.xml @ 5:befb1da9de9a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
author iuc
date Thu, 16 Oct 2025 20:11:34 +0000
parents eeb725655afc
children 0b41709046cf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
1 <tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
0
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
2 <description>index builder</description>
5
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
3 <macros>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
4 <token name="@TOOL_VERSION@">1.3.0</token>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
5 <token name="@VERSION_SUFFIX@">1</token>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
6 <token name="@PROFILE@">24.0</token>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
7 <token name="@IDX_VERSION@">q7</token>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
8 </macros>
0
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
9 <requirements>
5
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
10 <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
0
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
11 </requirements>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
12 <command detect_errors="exit_code"><![CDATA[
5
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
13 ## https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
14 ## https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
15
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
16 #for $transcripts in $transcriptome.fields.path.split(",")
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
17 (zcat '$transcripts' 2>/dev/null || cat '$transcripts') >> gentrome.fa &&
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
18 #end for
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
19 (zcat '$all_fasta_source.fields.path' 2>/dev/null || cat '$all_fasta_source.fields.path') >> gentrome.fa &&
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
20
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
21 (zcat '$all_fasta_source.fields.path' 2>/dev/null || cat '$all_fasta_source.fields.path') | awk '{if($1 ~ /^>/) print $1}' | cut -c2- | tr -d " " > decoys.txt &&
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
22
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
23 mkdir '$out_file.extra_files_path' &&
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
24
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
25 salmon index
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
26 -k $kmer_size
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
27 -t gentrome.fa
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
28 -d decoys.txt
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
29 -i '$out_file.extra_files_path'
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
30 -p "\${GALAXY_SLOTS:-12}"
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
31 $gencode
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
32 &&
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
33
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
34 cp '$dmjson' '$out_file'
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
35 ]]></command>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
36 <configfiles>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
37 <configfile name="dmjson"><![CDATA[{
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
38 #if str($sequence_id).strip() == ""
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
39 #set sequence_id = $all_fasta_source.fields.dbkey
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
40 #end if
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
41 #if str($sequence_name).strip() == ""
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
42 #set sequence_name = $all_fasta_source.fields.dbkey
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
43 #end if
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
44
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
45 "data_tables":{
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
46 "salmon_indexes_versioned":[
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
47 {
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
48 "value": "$sequence_id",
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
49 "dbkey": "$all_fasta_source.fields.dbkey",
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
50 "name": "$sequence_name",
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
51 "path": "$out_file.extra_files_path",
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
52 "version": "@IDX_VERSION@"
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
53 }
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
54 ]
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
55 }
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
56 }]]></configfile>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
57 </configfiles>
0
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
58 <inputs>
5
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
59 <param label="Transcriptome sequences" name="transcriptome" optional="false" type="select">
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
60 <options from_data_table="transcriptomes" />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
61 </param>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
62 <param label="Genome" name="all_fasta_source" optional="false" type="select">
0
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
63 <options from_data_table="all_fasta" />
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
64 </param>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
65 <param name="sequence_name" type="text" value="" label="Name of sequence" />
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
66 <param name="sequence_id" type="text" value="" label="ID for sequence" />
5
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
67 <param name="kmer_size" type="integer" optional='true' value="31" max="32" label="The size of the k-mer on which the index is built"
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
68 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be. We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE ">
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
69 <validator type="expression" message="Only odd values">value % 2 == 1</validator>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
70 </param>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
71 <param name="gencode" type="boolean" label="Transcript sequences are in gencode format" truevalue="--gencode" falsevalue="" checked="false" help="Will split the transcript name at the first '|' character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF."/>
0
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
72 </inputs>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
73 <outputs>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
74 <data name="out_file" format="data_manager_json" />
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
75 </outputs>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
76 <tests>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
77 <test>
5
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
78 <param name="transcriptome" value="phiX174"/>
0
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
79 <param name="all_fasta_source" value="phiX174"/>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
80 <param name="sequence_name" value="sequence_name"/>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
81 <param name="sequence_id" value="sequence_id"/>
1
d6fae6adc2b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit dcd9b028532258b62cfe15b60d5bef05cac9ed69"
iuc
parents: 0
diff changeset
82 <output name="out_file">
d6fae6adc2b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit dcd9b028532258b62cfe15b60d5bef05cac9ed69"
iuc
parents: 0
diff changeset
83 <assert_contents>
5
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
84 <has_text text='"salmon_indexes_versioned"' />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
85 <has_text text='"dbkey": "phiX174"' />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
86 <has_text text='"name": "sequence_name"' />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
87 <has_text text='"value": "sequence_id"' />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
88 <has_text text='"version": "q7"' />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
89 <has_text text='"path":' />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
90 </assert_contents>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
91 </output>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
92 </test>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
93 <test>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
94 <param name="transcriptome" value="phiX174"/>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
95 <param name="all_fasta_source" value="phiX174"/>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
96 <param name="sequence_name" value=""/>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
97 <param name="sequence_id" value=""/>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
98 <output name="out_file">
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
99 <assert_contents>
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
100 <has_text text='"salmon_indexes_versioned"' />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
101 <has_text text='"dbkey": "phiX174"' />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
102 <has_text text='"name": "phiX174"' />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
103 <has_text text='"value": "phiX174"' />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
104 <has_text text='"version": "q7"' />
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
105 <has_text text='"path":' />
1
d6fae6adc2b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit dcd9b028532258b62cfe15b60d5bef05cac9ed69"
iuc
parents: 0
diff changeset
106 </assert_contents>
d6fae6adc2b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit dcd9b028532258b62cfe15b60d5bef05cac9ed69"
iuc
parents: 0
diff changeset
107 </output>
0
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
108 </test>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
109 </tests>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
110 <help>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
111 <![CDATA[
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
112 .. class:: infomark
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
113
5
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
114 Indices are constructed as described here: https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
115
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
116 See also https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
117
befb1da9de9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_salmon_index_builder commit aed25572a6ac6a1f8acc72bb25ed3c337a623696
iuc
parents: 3
diff changeset
118 **Notice:** If you leave name, description, or id blank, it the dbkey of the genome will be used.
0
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
119 ]]>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
120 </help>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
121 <citations>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
122 <citation type="doi">https://doi.org/10.1038/nmeth.4197</citation>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
123 </citations>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
parents:
diff changeset
124 </tool>